\chapter{Accessing NCBI's Entrez databases}
\label{chapter:entrez}

Entrez (\url{http://www.ncbi.nlm.nih.gov/Entrez}) is a data retrieval system that provides users access to NCBI's databases such as PubMed, GenBank, GEO, and many others. You can access Entrez from a web browser to manually enter queries, or you can use Biopython's \verb+Bio.Entrez+ module for programmatic access to Entrez. The latter allows you for example to search PubMed or download GenBank records from within a Python script.

The \verb+Bio.Entrez+ module makes use of the Entrez Programming Utilities (also known as EUtils), consisting of eight tools that are described in detail on NCBI's page at \url{http://www.ncbi.nlm.nih.gov/entrez/utils/}.
Each of these tools corresponds to one Python function in the \verb+Bio.Entrez+ module, as described in the sections below. This module makes sure that the correct URL is used for the queries, and that not more than one request is made every three seconds, as required by NCBI.

The output returned by the Entrez Programming Utilities is typically in XML format. To parse such output, you have several options:
\begin{enumerate}
  \item Use \verb+Bio.Entrez+'s parser to parse the XML output into a Python object;
  \item Use the DOM (Document Object Model) parser in Python's standard library;
  \item Use the SAX (Simple API for XML) parser in Python's standard library;
  \item Read the XML output as raw text, and parse it by string searching and manipulation.
\end{enumerate}
For the DOM and SAX parsers, see the Python documentation. The parser in \verb+Bio.Entrez+ is discussed below.

NCBI uses DTD (Document Type Definition) files to describe the structure of the information contained in XML files. Most of the DTD files used by NCBI are included in the Biopython distribution. The \verb+Bio.Entrez+ parser makes use of the DTD files when parsing an XML file returned by NCBI Entrez.

Occasionally, you may find that the DTD file associated with a specific XML file is missing in the Biopython distribution. In particular, this may happen when NCBI updates its DTD files. If this happens, \verb+Entrez.read+ will show a warning message with the name and URL of the missing DTD file. The parser will proceed to access the missing DTD file through the internet, allowing the parsing of the XML file to continue.  However, the parser is much faster if the DTD file is available locally. For this purpose, please download the DTD file from the URL in the warning message and place it in the directory \verb+...site-packages/Bio/Entrez/DTDs+, containing the other DTD files.  If you don't have write access to this directory, you can also place the DTD file in \verb+~/.biopython/Bio/Entrez/DTDs+, where \verb+~+ represents your home directory. Since this directory is read before the directory \verb+...site-packages/Bio/Entrez/DTDs+, you can also put newer versions of DTD files there if the ones in \verb+...site-packages/Bio/Entrez/DTDs+ become outdated. Alternatively, if you installed Biopython from source, you can add the DTD file to the source code's \verb+Bio/Entrez/DTDs+ directory, and reinstall Biopython. This will install the new DTD file in the correct location together with the other DTD files.

The Entrez Programming Utilities can also generate output in other formats, such as the Fasta or GenBank file formats for sequence databases, or the MedLine format for the literature database, discussed in Section~\ref{sec:entrez-specialized-parsers}.

\section{Entrez Guidelines}
\label{sec:entrez-guidelines}
Before using Biopython to access the NCBI's online resources (via \verb|Bio.Entrez| or some of the other modules), please read the
\href{http://www.ncbi.nlm.nih.gov/books/NBK25497/#chapter2.Usage_Guidelines_and_Requiremen}{NCBI's Entrez User Requirements}.
If the NCBI finds you are abusing their systems, they can and will ban your access!

To paraphrase:

\begin{itemize}
\item For any series of more than 100 requests, do this at weekends or outside USA peak times.  This is up to you to obey.
\item Use the \url{http://eutils.ncbi.nlm.nih.gov} address, not the standard NCBI Web address.  Biopython uses this web address.
\item Make no more than three requests every seconds (relaxed from at most one request every three seconds in early 2009).  This is automatically enforced by Biopython.
\item Use the optional email parameter so the NCBI can contact you if there is a problem.  You can either explicitly set this as a parameter with each call to Entrez (e.g. include {\tt email="A.N.Other@example.com"} in the argument list), or you can set a global email address:
\begin{verbatim}
>>> from Bio import Entrez
>>> Entrez.email = "A.N.Other@example.com"
\end{verbatim}
{\tt Bio.Entrez} will then use this email address with each call to Entrez.  The {\tt example.com} address is a reserved domain name specifically for documentation (RFC 2606).  Please DO NOT use a random email -- it's better not to give an email at all. The email parameter will be mandatory from June 1, 2010. In case of excessive usage, NCBI will attempt to contact a user at the e-mail address provided prior to blocking access to the E-utilities.
\item If you are using Biopython within some larger software suite, use the tool parameter to specify this.  You can either explicitly set the tool name as a parameter with each call to Entrez (e.g. include {\tt tool="MyLocalScript"} in the argument list), or you can set a global tool name:
\begin{verbatim}
>>> from Bio import Entrez
>>> Entrez.tool = "MyLocalScript"
\end{verbatim}
The tool parameter will default to Biopython.
\item For large queries, the NCBI also recommend using their session history feature (the WebEnv session cookie string, see Section~\ref{sec:entrez-webenv}).  This is only slightly more complicated.
\end{itemize}

In conclusion, be sensible with your usage levels.  If you plan to download lots of data, consider other options.  For example, if you want easy access to all the human genes, consider fetching each chromosome by FTP as a GenBank file, and importing these into your own BioSQL database (see Section~\ref{sec:BioSQL}).

\section{EInfo: Obtaining information about the Entrez databases}
\label{sec:entrez-einfo}
EInfo provides field index term counts, last update, and available links for each of NCBI's databases. In addition, you can use EInfo to obtain a list of all database names accessible through the Entrez utilities:
\begin{verbatim}
>>> from Bio import Entrez
>>> Entrez.email = "A.N.Other@example.com"     # Always tell NCBI who you are
>>> handle = Entrez.einfo()
>>> result = handle.read()
\end{verbatim}
The variable \verb+result+ now contains a list of databases in XML format:
\begin{verbatim}
>>> print(result)
<?xml version="1.0"?>
<!DOCTYPE eInfoResult PUBLIC "-//NLM//DTD eInfoResult, 11 May 2002//EN"
 "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eInfo_020511.dtd">
<eInfoResult>
<DbList>
        <DbName>pubmed</DbName>
        <DbName>protein</DbName>
        <DbName>nucleotide</DbName>
        <DbName>nuccore</DbName>
        <DbName>nucgss</DbName>
        <DbName>nucest</DbName>
        <DbName>structure</DbName>
        <DbName>genome</DbName>
        <DbName>books</DbName>
        <DbName>cancerchromosomes</DbName>
        <DbName>cdd</DbName>
        <DbName>gap</DbName>
        <DbName>domains</DbName>
        <DbName>gene</DbName>
        <DbName>genomeprj</DbName>
        <DbName>gensat</DbName>
        <DbName>geo</DbName>
        <DbName>gds</DbName>
        <DbName>homologene</DbName>
        <DbName>journals</DbName>
        <DbName>mesh</DbName>
        <DbName>ncbisearch</DbName>
        <DbName>nlmcatalog</DbName>
        <DbName>omia</DbName>
        <DbName>omim</DbName>
        <DbName>pmc</DbName>
        <DbName>popset</DbName>
        <DbName>probe</DbName>
        <DbName>proteinclusters</DbName>
        <DbName>pcassay</DbName>
        <DbName>pccompound</DbName>
        <DbName>pcsubstance</DbName>
        <DbName>snp</DbName>
        <DbName>taxonomy</DbName>
        <DbName>toolkit</DbName>
        <DbName>unigene</DbName>
        <DbName>unists</DbName>
</DbList>
</eInfoResult>
\end{verbatim}

Since this is a fairly simple XML file, we could extract the information it contains simply by string searching. Using \verb+Bio.Entrez+'s parser instead, we can directly parse this XML file into a Python object:
\begin{verbatim}
>>> from Bio import Entrez
>>> handle = Entrez.einfo()
>>> record = Entrez.read(handle)
\end{verbatim}
Now \verb+record+ is a dictionary with exactly one key:
\begin{verbatim}
>>> record.keys()
[u'DbList']
\end{verbatim}
The values stored in this key is the list of database names shown in the XML above:
\begin{verbatim}
>>> record["DbList"]
['pubmed', 'protein', 'nucleotide', 'nuccore', 'nucgss', 'nucest',
 'structure', 'genome', 'books', 'cancerchromosomes', 'cdd', 'gap',
 'domains', 'gene', 'genomeprj', 'gensat', 'geo', 'gds', 'homologene',
 'journals', 'mesh', 'ncbisearch', 'nlmcatalog', 'omia', 'omim', 'pmc',
 'popset', 'probe', 'proteinclusters', 'pcassay', 'pccompound',
 'pcsubstance', 'snp', 'taxonomy', 'toolkit', 'unigene', 'unists']
\end{verbatim}

For each of these databases, we can use EInfo again to obtain more information:
\begin{verbatim}
>>> handle = Entrez.einfo(db="pubmed")
>>> record = Entrez.read(handle)
>>> record["DbInfo"]["Description"]
'PubMed bibliographic record'
>>> record["DbInfo"]["Count"]
'17989604'
>>> record["DbInfo"]["LastUpdate"]
'2008/05/24 06:45'
\end{verbatim}
Try \verb+record["DbInfo"].keys()+ for other information stored in this record.
One of the most useful is a list of possible search fields for use with ESearch:

\begin{verbatim}
>>> for field in record["DbInfo"]["FieldList"]:
...     print("%(Name)s, %(FullName)s, %(Description)s" % field)
ALL, All Fields, All terms from all searchable fields
UID, UID, Unique number assigned to publication
FILT, Filter, Limits the records
TITL, Title, Words in title of publication
WORD, Text Word, Free text associated with publication
MESH, MeSH Terms, Medical Subject Headings assigned to publication
MAJR, MeSH Major Topic, MeSH terms of major importance to publication
AUTH, Author, Author(s) of publication
JOUR, Journal, Journal abbreviation of publication
AFFL, Affiliation, Author's institutional affiliation and address
...
\end{verbatim}

That's a long list, but indirectly this tells you that for the PubMed
database, you can do things like \texttt{Jones[AUTH]} to search the
author field, or \texttt{Sanger[AFFL]} to restrict to authors at the
Sanger Centre. This can be very handy - especially if you are not so
familiar with a particular database.

\section{ESearch: Searching the Entrez databases}
\label{sec:entrez-esearch}
To search any of these databases, we use \verb+Bio.Entrez.esearch()+. For example, let's search in PubMed for publications related to Biopython:
\begin{verbatim}
>>> from Bio import Entrez
>>> Entrez.email = "A.N.Other@example.com"     # Always tell NCBI who you are
>>> handle = Entrez.esearch(db="pubmed", term="biopython")
>>> record = Entrez.read(handle)
>>> record["IdList"]
['19304878', '18606172', '16403221', '16377612', '14871861', '14630660', '12230038']
\end{verbatim}
In this output, you see seven PubMed IDs (including 19304878 which is the PMID for the Biopython application note), which can be retrieved by EFetch (see section \ref{sec:efetch}).

You can also use ESearch to search GenBank. Here we'll do a quick
search for the \emph{matK} gene in \emph{Cypripedioideae} orchids
(see Section~\ref{sec:entrez-einfo} about EInfo for one way to
find out which fields you can search in each Entrez database):

\begin{verbatim}
>>> handle = Entrez.esearch(db="nucleotide", term="Cypripedioideae[Orgn] AND matK[Gene]")
>>> record = Entrez.read(handle)
>>> record["Count"]
'25'
>>> record["IdList"]
['126789333', '37222967', '37222966', '37222965', ..., '61585492']
\end{verbatim}

\noindent Each of the IDs (126789333, 37222967, 37222966, \ldots) is a GenBank identifier.
See section~\ref{sec:efetch} for information on how to actually download these GenBank records.

Note that instead of a species name like \texttt{Cypripedioideae[Orgn]}, you can restrict the search using an NCBI taxon identifier, here this would be \texttt{txid158330[Orgn]}.  This isn't currently documented on the ESearch help page - the NCBI explained this in reply to an email query.  You can often deduce the search term formatting by playing with the Entrez web interface.  For example, including \texttt{complete[prop]} in a genome search restricts to just completed genomes.

As a final example, let's get a list of computational journal titles:
\begin{verbatim}
>>> handle = Entrez.esearch(db="nlmcatalog", term="computational[Journal]", retmax='20')
>>> record = Entrez.read(handle)
>>> print("{} computational journals found".format(record["Count"]))
117 computational Journals found
>>> print("The first 20 are\n{}".format(record['IdList']))
['101660833', '101664671', '101661657', '101659814', '101657941',
 '101653734', '101669877', '101649614', '101647835', '101639023',
 '101627224', '101647801', '101589678', '101585369', '101645372',
 '101586429', '101582229', '101574747', '101564639', '101671907']
\end{verbatim}
Again, we could use EFetch to obtain more information for each of these journal IDs.

ESearch has many useful options --- see the \href{https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch}{ESearch help page} for more information.

\section{EPost: Uploading a list of identifiers}
EPost uploads a list of UIs for use in subsequent search strategies; see the
\href{http://www.ncbi.nlm.nih.gov/entrez/query/static/epost\_help.html}{EPost help page} for more information. It is available from Biopython through
the \verb+Bio.Entrez.epost()+ function.

To give an example of when this is useful, suppose you have a long list of IDs
you want to download using EFetch (maybe sequences, maybe citations --
anything). When you make a  request with EFetch your list of IDs, the database
etc, are all turned into a long URL sent to the server.  If your list of IDs is
long, this URL gets long, and long URLs can break (e.g. some proxies don't
cope well).

Instead, you can break this up into two steps, first uploading the list of IDs
using EPost (this uses an ``HTML post'' internally, rather than an ``HTML get'',
getting round the long URL problem).  With the history support, you can then
refer to this long list of IDs, and download the associated data with EFetch.

Let's look at a simple example to see how EPost works -- uploading some PubMed identifiers:
\begin{verbatim}
>>> from Bio import Entrez
>>> Entrez.email = "A.N.Other@example.com"     # Always tell NCBI who you are
>>> id_list = ["19304878", "18606172", "16403221", "16377612", "14871861", "14630660"]
>>> print(Entrez.epost("pubmed", id=",".join(id_list)).read())
<?xml version="1.0"?>
<!DOCTYPE ePostResult PUBLIC "-//NLM//DTD ePostResult, 11 May 2002//EN"
 "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/ePost_020511.dtd">
<ePostResult>
	<QueryKey>1</QueryKey>
	<WebEnv>NCID_01_206841095_130.14.22.101_9001_1242061629</WebEnv>
</ePostResult>
\end{verbatim}
\noindent The returned XML includes two important strings, \verb|QueryKey| and \verb|WebEnv| which together define your history session.
You would extract these values for use with another Entrez call such as EFetch:
\begin{verbatim}
>>> from Bio import Entrez
>>> Entrez.email = "A.N.Other@example.com"     # Always tell NCBI who you are
>>> id_list = ["19304878", "18606172", "16403221", "16377612", "14871861", "14630660"]
>>> search_results = Entrez.read(Entrez.epost("pubmed", id=",".join(id_list)))
>>> webenv = search_results["WebEnv"]
>>> query_key = search_results["QueryKey"]
\end{verbatim}
\noindent Section~\ref{sec:entrez-webenv} shows how to use the history feature.

\section{ESummary: Retrieving summaries from primary IDs}
ESummary retrieves document summaries from a list of primary IDs (see the  \href{http://www.ncbi.nlm.nih.gov/entrez/query/static/esummary\_help.html}{ESummary help page} for more information). In Biopython, ESummary is available as \verb+Bio.Entrez.esummary()+. Using the search result above, we can for example find out more about the journal with ID 30367:
\begin{verbatim}
>>> from Bio import Entrez
>>> Entrez.email = "A.N.Other@example.com"     # Always tell NCBI who you are
>>> handle = Entrez.esummary(db="nlmcatalog", id="101660833")
>>> record = Entrez.read(handle)
>>> info = record[0]['TitleMainList'][0]
>>> print("Journal info\nid: {}\nTitle: {}".format(record[0]["Id"], info["Title"]))
Journal info
id: 101660833
Title: IEEE transactions on computational imaging.
\end{verbatim}

\section{EFetch: Downloading full records from Entrez}
\label{sec:efetch}

EFetch is what you use when you want to retrieve a full record from Entrez.
This covers several possible databases, as described on the main \href{http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetch_help.html}{EFetch Help page}.

For most of their databases, the NCBI support several different file formats. Requesting a specific file format from Entrez using \verb|Bio.Entrez.efetch()| requires specifying the \verb|rettype| and/or \verb|retmode| optional arguments.  The different combinations are described for each database type on the pages linked to on \href{http://www.ncbi.nlm.nih.gov/entrez/query/static/efetch_help.html}{NCBI efetch webpage} (e.g. \href{http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/efetchlit_help.html}{literature}, \href{http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/efetchseq_help.html}{sequences} and \href{http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/efetchtax_help.html}{taxonomy}).

One common usage is downloading sequences in the FASTA or GenBank/GenPept plain text formats (which can then be parsed with \verb|Bio.SeqIO|, see Sections~\ref{sec:SeqIO_GenBank_Online} and~\ref{sec:efetch}). From the \emph{Cypripedioideae} example above, we can download GenBank record 186972394 using \verb+Bio.Entrez.efetch+:

\begin{verbatim}
>>> from Bio import Entrez
>>> Entrez.email = "A.N.Other@example.com"     # Always tell NCBI who you are
>>> handle = Entrez.efetch(db="nucleotide", id="186972394", rettype="gb", retmode="text")
>>> print(handle.read())
LOCUS       EU490707                1302 bp    DNA     linear   PLN 05-MAY-2008
DEFINITION  Selenipedium aequinoctiale maturase K (matK) gene, partial cds;
            chloroplast.
ACCESSION   EU490707
VERSION     EU490707.1  GI:186972394
KEYWORDS    .
SOURCE      chloroplast Selenipedium aequinoctiale
  ORGANISM  Selenipedium aequinoctiale
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; Liliopsida; Asparagales; Orchidaceae;
            Cypripedioideae; Selenipedium.
REFERENCE   1  (bases 1 to 1302)
  AUTHORS   Neubig,K.M., Whitten,W.M., Carlsward,B.S., Blanco,M.A.,
            Endara,C.L., Williams,N.H. and Moore,M.J.
  TITLE     Phylogenetic utility of ycf1 in orchids
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1302)
  AUTHORS   Neubig,K.M., Whitten,W.M., Carlsward,B.S., Blanco,M.A.,
            Endara,C.L., Williams,N.H. and Moore,M.J.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-FEB-2008) Department of Botany, University of
            Florida, 220 Bartram Hall, Gainesville, FL 32611-8526, USA
FEATURES             Location/Qualifiers
     source          1..1302
                     /organism="Selenipedium aequinoctiale"
                     /organelle="plastid:chloroplast"
                     /mol_type="genomic DNA"
                     /specimen_voucher="FLAS:Blanco 2475"
                     /db_xref="taxon:256374"
     gene            <1..>1302
                     /gene="matK"
     CDS             <1..>1302
                     /gene="matK"
                     /codon_start=1
                     /transl_table=11
                     /product="maturase K"
                     /protein_id="ACC99456.1"
                     /db_xref="GI:186972395"
                     /translation="IFYEPVEIFGYDNKSSLVLVKRLITRMYQQNFLISSVNDSNQKG
                     FWGHKHFFSSHFSSQMVSEGFGVILEIPFSSQLVSSLEEKKIPKYQNLRSIHSIFPFL
                     EDKFLHLNYVSDLLIPHPIHLEILVQILQCRIKDVPSLHLLRLLFHEYHNLNSLITSK
                     KFIYAFSKRKKRFLWLLYNSYVYECEYLFQFLRKQSSYLRSTSSGVFLERTHLYVKIE
                     HLLVVCCNSFQRILCFLKDPFMHYVRYQGKAILASKGTLILMKKWKFHLVNFWQSYFH
                     FWSQPYRIHIKQLSNYSFSFLGYFSSVLENHLVVRNQMLENSFIINLLTKKFDTIAPV
                     ISLIGSLSKAQFCTVLGHPISKPIWTDFSDSDILDRFCRICRNLCRYHSGSSKKQVLY
                     RIKYILRLSCARTLARKHKSTVRTFMRRLGSGLLEEFFMEEE"
ORIGIN
        1 attttttacg aacctgtgga aatttttggt tatgacaata aatctagttt agtacttgtg
       61 aaacgtttaa ttactcgaat gtatcaacag aattttttga tttcttcggt taatgattct
      121 aaccaaaaag gattttgggg gcacaagcat tttttttctt ctcatttttc ttctcaaatg
      181 gtatcagaag gttttggagt cattctggaa attccattct cgtcgcaatt agtatcttct
      241 cttgaagaaa aaaaaatacc aaaatatcag aatttacgat ctattcattc aatatttccc
      301 tttttagaag acaaattttt acatttgaat tatgtgtcag atctactaat accccatccc
      361 atccatctgg aaatcttggt tcaaatcctt caatgccgga tcaaggatgt tccttctttg
      421 catttattgc gattgctttt ccacgaatat cataatttga atagtctcat tacttcaaag
      481 aaattcattt acgccttttc aaaaagaaag aaaagattcc tttggttact atataattct
      541 tatgtatatg aatgcgaata tctattccag tttcttcgta aacagtcttc ttatttacga
      601 tcaacatctt ctggagtctt tcttgagcga acacatttat atgtaaaaat agaacatctt
      661 ctagtagtgt gttgtaattc ttttcagagg atcctatgct ttctcaagga tcctttcatg
      721 cattatgttc gatatcaagg aaaagcaatt ctggcttcaa agggaactct tattctgatg
      781 aagaaatgga aatttcatct tgtgaatttt tggcaatctt attttcactt ttggtctcaa
      841 ccgtatagga ttcatataaa gcaattatcc aactattcct tctcttttct ggggtatttt
      901 tcaagtgtac tagaaaatca tttggtagta agaaatcaaa tgctagagaa ttcatttata
      961 ataaatcttc tgactaagaa attcgatacc atagccccag ttatttctct tattggatca
     1021 ttgtcgaaag ctcaattttg tactgtattg ggtcatccta ttagtaaacc gatctggacc
     1081 gatttctcgg attctgatat tcttgatcga ttttgccgga tatgtagaaa tctttgtcgt
     1141 tatcacagcg gatcctcaaa aaaacaggtt ttgtatcgta taaaatatat acttcgactt
     1201 tcgtgtgcta gaactttggc acggaaacat aaaagtacag tacgcacttt tatgcgaaga
     1261 ttaggttcgg gattattaga agaattcttt atggaagaag aa
//
\end{verbatim}

The arguments \verb+rettype="gb"+ and \verb+retmode="text"+ let us download this record in the GenBank format.

Note that until Easter 2009, the Entrez EFetch API let you use ``genbank'' as the
return type, however the NCBI now insist on using the official return types of
``gb'' or ``gbwithparts'' (or ``gp'' for proteins) as described on online.
Also not that until Feb 2012, the Entrez EFetch API would default to returning
plain text files, but now defaults to XML.

Alternatively, you could for example use \verb+rettype="fasta"+ to get the Fasta-format; see the \href{http://www.ncbi.nlm.nih.gov/entrez/query/static/efetchseq\_help.html}{EFetch Sequences Help page} for other options. Remember -- the available formats depend on which database you are downloading from - see the main \href{http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetch\_help.html}{EFetch Help page}.

If you fetch the record in one of the formats accepted by \verb+Bio.SeqIO+ (see Chapter~\ref{chapter:Bio.SeqIO}), you could directly parse it into a \verb+SeqRecord+:

\begin{verbatim}
>>> from Bio import Entrez, SeqIO
>>> handle = Entrez.efetch(db="nucleotide", id="186972394", rettype="gb", retmode="text")
>>> record = SeqIO.read(handle, "genbank")
>>> handle.close()
>>> print(record)
ID: EU490707.1
Name: EU490707
Description: Selenipedium aequinoctiale maturase K (matK) gene, partial cds; chloroplast.
Number of features: 3
...
Seq('ATTTTTTACGAACCTGTGGAAATTTTTGGTTATGACAATAAATCTAGTTTAGTA...GAA', IUPACAmbiguousDNA())
\end{verbatim}

Note that a more typical use would be to save the sequence data to a local file, and \emph{then} parse it with \verb|Bio.SeqIO|.  This can save you having to re-download the same file repeatedly while working on your script, and places less load on the NCBI's servers.  For example:

\begin{verbatim}
import os
from Bio import SeqIO
from Bio import Entrez
Entrez.email = "A.N.Other@example.com"  # Always tell NCBI who you are
filename = "gi_186972394.gbk"
if not os.path.isfile(filename):
    # Downloading...
    net_handle = Entrez.efetch(db="nucleotide", id="186972394", rettype="gb", retmode="text")
    out_handle = open(filename, "w")
    out_handle.write(net_handle.read())
    out_handle.close()
    net_handle.close()
    print("Saved")

print("Parsing...")
record = SeqIO.read(filename, "genbank")
print(record)
\end{verbatim}

To get the output in XML format, which you can parse using the \verb+Bio.Entrez.read()+ function, use \verb+retmode="xml"+:

\begin{verbatim}
>>> from Bio import Entrez
>>> handle = Entrez.efetch(db="nucleotide", id="186972394", retmode="xml")
>>> record = Entrez.read(handle)
>>> handle.close()
>>> record[0]["GBSeq_definition"]
'Selenipedium aequinoctiale maturase K (matK) gene, partial cds; chloroplast'
>>> record[0]["GBSeq_source"]
'chloroplast Selenipedium aequinoctiale'
\end{verbatim}

So, that dealt with sequences. For examples of parsing file formats specific to the other databases (e.g. the \verb+MEDLINE+ format used in PubMed), see Section~\ref{sec:entrez-specialized-parsers}.

If you want to perform a search with \verb|Bio.Entrez.esearch()|, and then download the records with \verb|Bio.Entrez.efetch()|, you should use the WebEnv history feature -- see Section~\ref{sec:entrez-webenv}.

\section{ELink: Searching for related items in NCBI Entrez}
\label{sec:elink}

ELink, available from Biopython as \verb+Bio.Entrez.elink()+, can be used to find related items in the NCBI Entrez databases. For example, you can us this to find nucleotide entries for an entry in the gene database,
and other cool stuff.

Let's use ELink to find articles related to the Biopython application note published in \textit{Bioinformatics} in 2009. The PubMed ID of this article is 19304878:

\begin{verbatim}
>>> from Bio import Entrez
>>> Entrez.email = "A.N.Other@example.com"
>>> pmid = "19304878"
>>> record = Entrez.read(Entrez.elink(dbfrom="pubmed", id=pmid))
\end{verbatim}

The \verb+record+ variable consists of a Python list, one for each database in which we searched. Since we specified only one PubMed ID to search for, \verb+record+ contains only one item. This item is a dictionary containing information about our search term, as well as all the related items that were found:

\begin{verbatim}
>>> record[0]["DbFrom"]
'pubmed'
>>> record[0]["IdList"]
['19304878']
\end{verbatim}

The \verb+"LinkSetDb"+ key contains the search results, stored as a list consisting of one item for each target database. In our search results, we only find hits in the PubMed database (although sub-divided into categories):

\begin{verbatim}
>>> len(record[0]["LinkSetDb"])
5
>>> for linksetdb in record[0]["LinkSetDb"]:
...     print(linksetdb["DbTo"], linksetdb["LinkName"], len(linksetdb["Link"]))
...
pubmed pubmed_pubmed 110
pubmed pubmed_pubmed_combined 6
pubmed pubmed_pubmed_five 6
pubmed pubmed_pubmed_reviews 5
pubmed pubmed_pubmed_reviews_five 5
\end{verbatim}

The actual search results are stored as under the \verb+"Link"+ key. In total, 110 items were found under
standard search.
Let's now at the first search result:
\begin{verbatim}
>>> record[0]["LinkSetDb"][0]["Link"][0]
{u'Id': '19304878'}
\end{verbatim}

\noindent This is the article we searched for, which doesn't help us much, so let's look at the second search result:

\begin{verbatim}
>>> record[0]["LinkSetDb"][0]["Link"][1]
{u'Id': '14630660'}
\end{verbatim}

\noindent This paper, with PubMed ID 14630660, is about the Biopython PDB parser.

We can use a loop to print out all PubMed IDs:
\begin{verbatim}
>>> for link in record[0]["LinkSetDb"][0]["Link"]:
...     print(link["Id"])
19304878
14630660
18689808
17121776
16377612
12368254
......
\end{verbatim}

Now that was nice, but personally I am often more interested to find out if a paper has been cited.
Well, ELink can do that too -- at least for journals in Pubmed Central (see Section~\ref{sec:elink-citations}).

For help on ELink, see the \href{http://www.ncbi.nlm.nih.gov/entrez/query/static/elink\_help.html}{ELink help page}.
There is an entire sub-page just for the \href{http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/entrezlinks.html}{link names}, describing how different databases can be cross referenced.

\section{EGQuery: Global Query - counts for search terms}
EGQuery provides counts for a search term in each of the Entrez databases (i.e. a global query). This is particularly useful to find out how many items your search terms would find in each database without actually performing lots of separate searches with ESearch (see the example in \ref{subsec:entrez_example_genbank} below).

In this example, we use \verb+Bio.Entrez.egquery()+ to obtain the counts for ``Biopython'':

\begin{verbatim}
>>> from Bio import Entrez
>>> Entrez.email = "A.N.Other@example.com"     # Always tell NCBI who you are
>>> handle = Entrez.egquery(term="biopython")
>>> record = Entrez.read(handle)
>>> for row in record["eGQueryResult"]:
...     print(row["DbName"], row["Count"])
...
pubmed 6
pmc 62
journals 0
...
\end{verbatim}
See the \href{http://www.ncbi.nlm.nih.gov/entrez/query/static/egquery\_help.html}{EGQuery help page} for more information.

\section{ESpell: Obtaining spelling suggestions}
ESpell retrieves spelling suggestions. In this example, we use \verb+Bio.Entrez.espell()+ to obtain the correct spelling of Biopython:

\begin{verbatim}
>>> from Bio import Entrez
>>> Entrez.email = "A.N.Other@example.com"     # Always tell NCBI who you are
>>> handle = Entrez.espell(term="biopythooon")
>>> record = Entrez.read(handle)
>>> record["Query"]
'biopythooon'
>>> record["CorrectedQuery"]
'biopython'
\end{verbatim}
See the \href{http://www.ncbi.nlm.nih.gov/entrez/query/static/espell\_help.html}{ESpell help page} for more information.
The main use of this is for GUI tools to provide automatic suggestions for search terms.

\section{Parsing huge Entrez XML files}

The \verb+Entrez.read+ function reads the entire XML file returned by Entrez into a single Python object, which is kept in memory. To parse Entrez XML files too large to fit in memory, you can use the function \verb+Entrez.parse+. This is a generator function that reads records in the XML file one by one. This function is only useful if the XML file reflects a Python list object (in other words, if \verb+Entrez.read+ on a computer with infinite memory resources would return a Python list).

For example, you can download the entire Entrez Gene database for a given organism as a file from NCBI's ftp site. These files can be very large. As an example, on September 4, 2009, the file \verb+Homo_sapiens.ags.gz+, containing the Entrez Gene database for human, had a size of 116576 kB. This file, which is in the \verb+ASN+ format, can be converted into an XML file using NCBI's \verb+gene2xml+ program (see NCBI's ftp site for more information):

\begin{verbatim}
gene2xml -b T -i Homo_sapiens.ags -o Homo_sapiens.xml
\end{verbatim}

The resulting XML file has a size of 6.1 GB. Attempting \verb+Entrez.read+ on this file will result in a \verb+MemoryError+ on many computers.

The XML file \verb+Homo_sapiens.xml+ consists of a list of Entrez gene records, each corresponding to one Entrez gene in human. \verb+Entrez.parse+ retrieves these gene records one by one. You can then print out or store the relevant information in each record by iterating over the records. For example, this script iterates over the Entrez gene records and prints out the gene numbers and names for all current genes:

\begin{verbatim}
>>> from Bio import Entrez
>>> handle = open("Homo_sapiens.xml")
>>> records = Entrez.parse(handle)

>>> for record in records:
...     status = record['Entrezgene_track-info']['Gene-track']['Gene-track_status']
...     if status.attributes['value']=='discontinued':
...         continue
...     geneid = record['Entrezgene_track-info']['Gene-track']['Gene-track_geneid']
...     genename = record['Entrezgene_gene']['Gene-ref']['Gene-ref_locus']
...     print(geneid, genename)
\end{verbatim}

This will print:
\begin{verbatim}
1 A1BG
2 A2M
3 A2MP
8 AA
9 NAT1
10 NAT2
11 AACP
12 SERPINA3
13 AADAC
14 AAMP
15 AANAT
16 AARS
17 AAVS1
...
\end{verbatim}


\section{Handling errors}

Three things can go wrong when parsing an XML file:
\begin{itemize}
\item The file may not be an XML file to begin with;
\item The file may end prematurely or otherwise be corrupted;
\item The file may be correct XML, but contain items that are not represented in the associated DTD.
\end{itemize}

The first case occurs if, for example, you try to parse a Fasta file as if it were an XML file:
\begin{verbatim}
>>> from Bio import Entrez
>>> handle = open("NC_005816.fna") # a Fasta file
>>> record = Entrez.read(handle)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python2.7/site-packages/Bio/Entrez/__init__.py", line 257, in read
    record = handler.read(handle)
  File "/usr/local/lib/python2.7/site-packages/Bio/Entrez/Parser.py", line 164, in read
    raise NotXMLError(e)
Bio.Entrez.Parser.NotXMLError: Failed to parse the XML data (syntax error: line 1, column 0). Please make sure that the input data are in XML format.
\end{verbatim}
Here, the parser didn't find the \verb|<?xml ...| tag with which an XML file is supposed to start, and therefore decides (correctly) that the file is not an XML file.

When your file is in the XML format but is corrupted (for example, by ending prematurely), the parser will raise a CorruptedXMLError.
Here is an example of an XML file that ends prematurely:
\begin{verbatim}
<?xml version="1.0"?>
<!DOCTYPE eInfoResult PUBLIC "-//NLM//DTD eInfoResult, 11 May 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eInfo_020511.dtd">
<eInfoResult>
<DbList>
        <DbName>pubmed</DbName>
        <DbName>protein</DbName>
        <DbName>nucleotide</DbName>
        <DbName>nuccore</DbName>
        <DbName>nucgss</DbName>
        <DbName>nucest</DbName>
        <DbName>structure</DbName>
        <DbName>genome</DbName>
        <DbName>books</DbName>
        <DbName>cancerchromosomes</DbName>
        <DbName>cdd</DbName>
\end{verbatim}
which will generate the following traceback:
\begin{verbatim}
>>> Entrez.read(handle)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python2.7/site-packages/Bio/Entrez/__init__.py", line 257, in read
    record = handler.read(handle)
  File "/usr/local/lib/python2.7/site-packages/Bio/Entrez/Parser.py", line 160, in read
    raise CorruptedXMLError(e)
Bio.Entrez.Parser.CorruptedXMLError: Failed to parse the XML data (no element found: line 16, column 0). Please make sure that the input data are not corrupted.

>>>
\end{verbatim}
Note that the error message tells you at what point in the XML file the error was detected.

The third type of error occurs if the XML file contains tags that do not have a description in the corresponding DTD file. This is an example of such an XML file:

\begin{verbatim}
<?xml version="1.0"?>
<!DOCTYPE eInfoResult PUBLIC "-//NLM//DTD eInfoResult, 11 May 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eInfo_020511.dtd">
<eInfoResult>
        <DbInfo>
        <DbName>pubmed</DbName>
        <MenuName>PubMed</MenuName>
        <Description>PubMed bibliographic record</Description>
        <Count>20161961</Count>
        <LastUpdate>2010/09/10 04:52</LastUpdate>
        <FieldList>
                <Field>
...
                </Field>
        </FieldList>
        <DocsumList>
                <Docsum>
                        <DsName>PubDate</DsName>
                        <DsType>4</DsType>
                        <DsTypeName>string</DsTypeName>
                </Docsum>
                <Docsum>
                        <DsName>EPubDate</DsName>
...
        </DbInfo>
</eInfoResult>
\end{verbatim}

In this file, for some reason the tag \verb|<DocsumList>| (and several others) are not listed in the DTD file \verb|eInfo_020511.dtd|, which is specified on the second line as the DTD for this XML file. By default, the parser will stop and raise a ValidationError if it cannot find some tag in the DTD:

\begin{verbatim}
>>> from Bio import Entrez
>>> handle = open("einfo3.xml")
>>> record = Entrez.read(handle)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python2.7/site-packages/Bio/Entrez/__init__.py", line 257, in read
    record = handler.read(handle)
  File "/usr/local/lib/python2.7/site-packages/Bio/Entrez/Parser.py", line 154, in read
    self.parser.ParseFile(handle)
  File "/usr/local/lib/python2.7/site-packages/Bio/Entrez/Parser.py", line 246, in startElementHandler
    raise ValidationError(name)
Bio.Entrez.Parser.ValidationError: Failed to find tag 'DocsumList' in the DTD. To skip all tags that are not represented in the DTD, please call Bio.Entrez.read or Bio.Entrez.parse with validate=False.
\end{verbatim}
Optionally, you can instruct the parser to skip such tags instead of raising a ValidationError. This is done by calling \verb|Entrez.read| or \verb|Entrez.parse| with the argument \verb|validate| equal to False:
\begin{verbatim}
>>> from Bio import Entrez
>>> handle = open("einfo3.xml")
>>> record = Entrez.read(handle, validate=False)
>>>
\end{verbatim}
Of course, the information contained in the XML tags that are not in the DTD are not present in the record returned by \verb|Entrez.read|.


\section{Specialized parsers}
\label{sec:entrez-specialized-parsers}

The \verb|Bio.Entrez.read()| function can parse most (if not all) XML output returned by Entrez. Entrez typically allows you to retrieve records in other formats, which may have some advantages compared to the XML format in terms of readability (or download size).

To request a specific file format from Entrez using \verb|Bio.Entrez.efetch()| requires specifying the \verb|rettype| and/or \verb|retmode| optional arguments.  The different combinations are described for each database type on the \href{http://www.ncbi.nlm.nih.gov/entrez/query/static/efetch_help.html}{NCBI efetch webpage}.

One obvious case is you may prefer to download sequences in the FASTA or GenBank/GenPept plain text formats (which can then be parsed with \verb|Bio.SeqIO|, see Sections~\ref{sec:SeqIO_GenBank_Online} and~\ref{sec:efetch}).  For the literature databases, Biopython contains a parser for the \verb+MEDLINE+ format used in PubMed.

\subsection{Parsing Medline records}
\label{subsec:entrez-and-medline}
You can find the Medline parser in \verb+Bio.Medline+. Suppose we want to parse the file \verb+pubmed_result1.txt+, containing one Medline record. You can find this file in Biopython's \verb+Tests\Medline+ directory. The file looks like this:

\begin{verbatim}
PMID- 12230038
OWN - NLM
STAT- MEDLINE
DA  - 20020916
DCOM- 20030606
LR  - 20041117
PUBM- Print
IS  - 1467-5463 (Print)
VI  - 3
IP  - 3
DP  - 2002 Sep
TI  - The Bio* toolkits--a brief overview.
PG  - 296-302
AB  - Bioinformatics research is often difficult to do with commercial software. The
      Open Source BioPerl, BioPython and Biojava projects provide toolkits with
...
\end{verbatim}
We first open the file and then parse it:
%doctest ../Tests/Medline
\begin{verbatim}
>>> from Bio import Medline
>>> with open("pubmed_result1.txt") as handle:
...    record = Medline.read(handle)
...
\end{verbatim}
The \verb+record+ now contains the Medline record as a Python dictionary:
%cont-doctest
\begin{verbatim}
>>> record["PMID"]
'12230038'
\end{verbatim}
%TODO - doctest wrapping?
\begin{verbatim}
>>> record["AB"]
'Bioinformatics research is often difficult to do with commercial software.
The Open Source BioPerl, BioPython and Biojava projects provide toolkits with
multiple functionality that make it easier to create customised pipelines or
analysis. This review briefly compares the quirks of the underlying languages
and the functionality, documentation, utility and relative advantages of the
Bio counterparts, particularly from the point of view of the beginning
biologist programmer.'
\end{verbatim}
The key names used in a Medline record can be rather obscure; use
\begin{verbatim}
>>> help(record)
\end{verbatim}
for a brief summary.

To parse a file containing multiple Medline records, you can use the \verb+parse+ function instead:
%doctest ../Tests/Medline
\begin{verbatim}
>>> from Bio import Medline
>>> with open("pubmed_result2.txt") as handle:
...     for record in Medline.parse(handle):
...         print(record["TI"])
...
A high level interface to SCOP and ASTRAL implemented in python.
GenomeDiagram: a python package for the visualization of large-scale genomic data.
Open source clustering software.
PDB file parser and structure class implemented in Python.
\end{verbatim}

Instead of parsing Medline records stored in files, you can also parse Medline records downloaded by \verb+Bio.Entrez.efetch+. For example, let's look at all Medline records in PubMed related to Biopython:
\begin{verbatim}
>>> from Bio import Entrez
>>> Entrez.email = "A.N.Other@example.com"     # Always tell NCBI who you are
>>> handle = Entrez.esearch(db="pubmed", term="biopython")
>>> record = Entrez.read(handle)
>>> record["IdList"]
['19304878', '18606172', '16403221', '16377612', '14871861', '14630660', '12230038']
\end{verbatim}
We now use \verb+Bio.Entrez.efetch+ to download these Medline records:
\begin{verbatim}
>>> idlist = record["IdList"]
>>> handle = Entrez.efetch(db="pubmed", id=idlist, rettype="medline", retmode="text")
\end{verbatim}
Here, we specify \verb+rettype="medline", retmode="text"+ to obtain the Medline records in plain-text Medline format. Now we use \verb+Bio.Medline+ to parse these records:
\begin{verbatim}
>>> from Bio import Medline
>>> records = Medline.parse(handle)
>>> for record in records:
...     print(record["AU"])
['Cock PJ', 'Antao T', 'Chang JT', 'Chapman BA', 'Cox CJ', 'Dalke A', ..., 'de Hoon MJ']
['Munteanu CR', 'Gonzalez-Diaz H', 'Magalhaes AL']
['Casbon JA', 'Crooks GE', 'Saqi MA']
['Pritchard L', 'White JA', 'Birch PR', 'Toth IK']
['de Hoon MJ', 'Imoto S', 'Nolan J', 'Miyano S']
['Hamelryck T', 'Manderick B']
['Mangalam H']
\end{verbatim}

For comparison, here we show an example using the XML format:
\begin{verbatim}
>>> idlist = record["IdList"]
>>> handle = Entrez.efetch(db="pubmed", id=idlist, rettype="medline", retmode="xml")
>>> records = Entrez.read(handle)
>>> for record in records:
...     print(record["MedlineCitation"]["Article"]["ArticleTitle"])
Biopython: freely available Python tools for computational molecular biology and
 bioinformatics.
Enzymes/non-enzymes classification model complexity based on composition, sequence,
 3D and topological indices.
A high level interface to SCOP and ASTRAL implemented in python.
GenomeDiagram: a python package for the visualization of large-scale genomic data.
Open source clustering software.
PDB file parser and structure class implemented in Python.
The Bio* toolkits--a brief overview.
\end{verbatim}

Note that in both of these examples, for simplicity we have naively combined ESearch and EFetch.
In this situation, the NCBI would expect you to use their history feature,
as illustrated in Section~\ref{sec:entrez-webenv}.


\subsection{Parsing GEO records}

GEO (\href{http://www.ncbi.nlm.nih.gov/geo/}{Gene Expression Omnibus})
is a data repository of high-throughput gene expression and hybridization
array data. The \verb|Bio.Geo| module can be used to parse GEO-formatted
data.

The following code fragment shows how to parse the example GEO file
\verb|GSE16.txt| into a record and print the record:

\begin{verbatim}
>>> from Bio import Geo
>>> handle = open("GSE16.txt")
>>> records = Geo.parse(handle)
>>> for record in records:
...     print(record)
\end{verbatim}

You can search the ``gds'' database (GEO datasets) with ESearch:

\begin{verbatim}
>>> from Bio import Entrez
>>> Entrez.email = "A.N.Other@example.com" # Always tell NCBI who you are
>>> handle = Entrez.esearch(db="gds", term="GSE16")
>>> record = Entrez.read(handle)
>>> record["Count"]
2
>>> record["IdList"]
['200000016', '100000028']
\end{verbatim}

From the Entrez website, UID ``200000016'' is GDS16 while the other hit
``100000028'' is for the associated platform, GPL28.  Unfortunately, at the
time of writing the NCBI don't seem to support downloading GEO files using
Entrez (not as XML, nor in the \textit{Simple Omnibus Format in Text} (SOFT)
format).

However, it is actually pretty straight forward to download the GEO files by FTP
from \url{ftp://ftp.ncbi.nih.gov/pub/geo/} instead.  In this case you might want
\url{ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/by_series/GSE16/GSE16_family.soft.gz}
(a compressed file, see the Python module gzip).

\subsection{Parsing UniGene records}

UniGene is an NCBI database of the transcriptome, with each UniGene record showing the set of transcripts that are associated with a particular gene in a specific organism. A typical UniGene record looks like this:

\begin{verbatim}
ID          Hs.2
TITLE       N-acetyltransferase 2 (arylamine N-acetyltransferase)
GENE        NAT2
CYTOBAND    8p22
GENE_ID     10
LOCUSLINK   10
HOMOL       YES
EXPRESS      bone| connective tissue| intestine| liver| liver tumor| normal| soft tissue/muscle tissue tumor| adult
RESTR_EXPR   adult
CHROMOSOME  8
STS         ACC=PMC310725P3 UNISTS=272646
STS         ACC=WIAF-2120 UNISTS=44576
STS         ACC=G59899 UNISTS=137181
...
STS         ACC=GDB:187676 UNISTS=155563
PROTSIM     ORG=10090; PROTGI=6754794; PROTID=NP_035004.1; PCT=76.55; ALN=288
PROTSIM     ORG=9796; PROTGI=149742490; PROTID=XP_001487907.1; PCT=79.66; ALN=288
PROTSIM     ORG=9986; PROTGI=126722851; PROTID=NP_001075655.1; PCT=76.90; ALN=288
...
PROTSIM     ORG=9598; PROTGI=114619004; PROTID=XP_519631.2; PCT=98.28; ALN=288

SCOUNT      38
SEQUENCE    ACC=BC067218.1; NID=g45501306; PID=g45501307; SEQTYPE=mRNA
SEQUENCE    ACC=NM_000015.2; NID=g116295259; PID=g116295260; SEQTYPE=mRNA
SEQUENCE    ACC=D90042.1; NID=g219415; PID=g219416; SEQTYPE=mRNA
SEQUENCE    ACC=D90040.1; NID=g219411; PID=g219412; SEQTYPE=mRNA
SEQUENCE    ACC=BC015878.1; NID=g16198419; PID=g16198420; SEQTYPE=mRNA
SEQUENCE    ACC=CR407631.1; NID=g47115198; PID=g47115199; SEQTYPE=mRNA
SEQUENCE    ACC=BG569293.1; NID=g13576946; CLONE=IMAGE:4722596; END=5'; LID=6989; SEQTYPE=EST; TRACE=44157214
...
SEQUENCE    ACC=AU099534.1; NID=g13550663; CLONE=HSI08034; END=5'; LID=8800; SEQTYPE=EST
//
\end{verbatim}

This particular record shows the set of transcripts (shown in the \verb+SEQUENCE+ lines) that originate from the human gene NAT2, encoding en N-acetyltransferase. The \verb+PROTSIM+ lines show proteins with significant similarity to NAT2, whereas the \verb+STS+ lines show the corresponding sequence-tagged sites in the genome.

To parse UniGene files, use the \verb+Bio.UniGene+ module:
\begin{verbatim}
>>> from Bio import UniGene
>>> input = open("myunigenefile.data")
>>> record = UniGene.read(input)
\end{verbatim}

The \verb+record+ returned by \verb+UniGene.read+ is a Python object with attributes corresponding to the fields in the UniGene record. For example,
\begin{verbatim}
>>> record.ID
"Hs.2"
>>> record.title
"N-acetyltransferase 2 (arylamine N-acetyltransferase)"
\end{verbatim}

The \verb+EXPRESS+ and \verb+RESTR_EXPR+ lines are stored as Python lists of strings:
\begin{verbatim}
['bone', 'connective tissue', 'intestine', 'liver', 'liver tumor', 'normal', 'soft tissue/muscle tissue tumor', 'adult']
\end{verbatim}

Specialized objects are returned for the \verb+STS+, \verb+PROTSIM+, and \verb+SEQUENCE+ lines, storing the keys shown in each line as attributes:
\begin{verbatim}
>>> record.sts[0].acc
'PMC310725P3'
>>> record.sts[0].unists
'272646'
\end{verbatim}
and similarly for the \verb+PROTSIM+ and \verb+SEQUENCE+ lines.

To parse a file containing more than one UniGene record, use the \verb+parse+ function in \verb+Bio.UniGene+:

\begin{verbatim}
>>> from Bio import UniGene
>>> input = open("unigenerecords.data")
>>> records = UniGene.parse(input)
>>> for record in records:
...     print(record.ID)
\end{verbatim}

\section{Using a proxy}

Normally you won't have to worry about using a proxy, but if this is an issue
on your network here is how to deal with it.  Internally, \verb|Bio.Entrez|
uses the standard Python library \verb|urllib| for accessing the NCBI servers.
This will check an environment variable called \verb|http_proxy| to configure
any simple proxy automatically.  Unfortunately this module does not support
the use of proxies which require authentication.

You may choose to set the \verb|http_proxy| environment variable once (how you
do this will depend on your operating system).  Alternatively you can set this
within Python at the start of your script, for example:

\begin{verbatim}
import os
os.environ["http_proxy"] = "http://proxyhost.example.com:8080"
\end{verbatim}

\noindent See the \href{http://www.python.org/doc/lib/module-urllib.html}
{urllib documentation} for more details.

\section{Examples}
\label{sec:entrez_examples}

\subsection{PubMed and Medline}
\label{subsec:pub_med}

If you are in the medical field or interested in human issues (and many times even if you are not!), PubMed (\url{http://www.ncbi.nlm.nih.gov/PubMed/}) is an excellent source of all kinds of goodies. So like other things, we'd like to be able to grab information from it and use it in Python scripts.

In this example, we will query PubMed for all articles having to do with orchids (see section~\ref{sec:orchids} for our motivation). We first check how many of such articles there are:

\begin{verbatim}
>>> from Bio import Entrez
>>> Entrez.email = "A.N.Other@example.com"     # Always tell NCBI who you are
>>> handle = Entrez.egquery(term="orchid")
>>> record = Entrez.read(handle)
>>> for row in record["eGQueryResult"]:
...     if row["DbName"]=="pubmed":
...         print(row["Count"])
463
\end{verbatim}

Now we use the \verb+Bio.Entrez.efetch+ function to download the PubMed IDs of these 463 articles:
\begin{verbatim}
>>> handle = Entrez.esearch(db="pubmed", term="orchid", retmax=463)
>>> record = Entrez.read(handle)
>>> idlist = record["IdList"]
>>> print(idlist)
\end{verbatim}


This returns a Python list containing all of the PubMed IDs of articles related to orchids:
\begin{verbatim}
['18680603', '18665331', '18661158', '18627489', '18627452', '18612381',
'18594007', '18591784', '18589523', '18579475', '18575811', '18575690',
...
\end{verbatim}

Now that we've got them, we obviously want to get the corresponding Medline records and extract the information from them. Here, we'll download the Medline records in the Medline flat-file format, and use the \verb+Bio.Medline+ module to parse them:
\begin{verbatim}
>>> from Bio import Medline
>>> handle = Entrez.efetch(db="pubmed", id=idlist, rettype="medline",
                           retmode="text")
>>> records = Medline.parse(handle)
\end{verbatim}

NOTE - We've just done a separate search and fetch here, the NCBI much prefer you to take advantage of their history support in this situation.  See Section~\ref{sec:entrez-webenv}.

Keep in mind that \verb+records+ is an iterator, so you can iterate through the records only once. If you want to save the records, you can convert them to a list:
\begin{verbatim}
>>> records = list(records)
\end{verbatim}

Let's now iterate over the records to print out some information about each record:
%TODO - Replace the print blank line with print()?
\begin{verbatim}
>>> for record in records:
...     print("title:", record.get("TI", "?"))
...     print("authors:", record.get("AU", "?"))
...     print("source:", record.get("SO", "?"))
...     print("")
\end{verbatim}

The output for this looks like:
\begin{verbatim}
title: Sex pheromone mimicry in the early spider orchid (ophrys sphegodes):
patterns of hydrocarbons as the key mechanism for pollination by sexual
deception [In Process Citation]
authors: ['Schiestl FP', 'Ayasse M', 'Paulus HF', 'Lofstedt C', 'Hansson BS',
'Ibarra F', 'Francke W']
source: J Comp Physiol [A] 2000 Jun;186(6):567-74
\end{verbatim}

Especially interesting to note is the list of authors, which is returned as a standard Python list. This makes it easy to manipulate and search using standard Python tools. For instance, we could loop through a whole bunch of entries searching for a particular author with code like the following:
\begin{verbatim}
>>> search_author = "Waits T"

>>> for record in records:
...     if not "AU" in record:
...         continue
...     if search_author in record["AU"]:
...         print("Author %s found: %s" % (search_author, record["SO"]))
\end{verbatim}

Hopefully this section gave you an idea of the power and flexibility of the Entrez and Medline interfaces and how they can be used together.

\subsection{Searching, downloading, and parsing Entrez Nucleotide records}
\label{subsec:entrez_example_genbank}

Here we'll show a simple example of performing a remote Entrez query. In section~\ref{sec:orchids} of the parsing examples, we talked about using NCBI's Entrez website to search the NCBI nucleotide databases for info on Cypripedioideae, our friends the lady slipper orchids. Now, we'll look at how to automate that process using a Python script. In this example, we'll just show how to connect, get the results, and parse them, with the Entrez module doing all of the work.

First, we use EGQuery to find out the number of results we will get before actually downloading them.  EGQuery will tell us how many search results were found in each of the databases, but for this example we are only interested in nucleotides:
\begin{verbatim}
>>> from Bio import Entrez
>>> Entrez.email = "A.N.Other@example.com"     # Always tell NCBI who you are
>>> handle = Entrez.egquery(term="Cypripedioideae")
>>> record = Entrez.read(handle)
>>> for row in record["eGQueryResult"]:
...     if row["DbName"]=="nuccore":
...         print(row["Count"])
814
\end{verbatim}

So, we expect to find 814 Entrez Nucleotide records (this is the number I obtained in 2008; it is likely to increase in the future). If you find some ridiculously high number of hits, you may want to reconsider if you really want to download all of them, which is our next step:
\begin{verbatim}
>>> from Bio import Entrez
>>> handle = Entrez.esearch(db="nucleotide", term="Cypripedioideae", retmax=814)
>>> record = Entrez.read(handle)
\end{verbatim}

Here, \verb+record+ is a Python dictionary containing the search results and some auxiliary information. Just for information, let's look at what is stored in this dictionary:
\begin{verbatim}
>>> print(record.keys())
[u'Count', u'RetMax', u'IdList', u'TranslationSet', u'RetStart', u'QueryTranslation']
\end{verbatim}
First, let's check how many results were found:
\begin{verbatim}
>>> print(record["Count"])
'814'
\end{verbatim}
which is the number we expected. The 814 results are stored in \verb+record['IdList']+:
\begin{verbatim}
>>> len(record["IdList"])
814
\end{verbatim}
Let's look at the first five results:
\begin{verbatim}
>>> record["IdList"][:5]
['187237168', '187372713', '187372690', '187372688', '187372686']
\end{verbatim}

\label{sec:entrez-batched-efetch}
We can download these records using \verb+efetch+.
While you could download these records one by one, to reduce the load on NCBI's servers, it is better to fetch a bunch of records at the same time, shown below.
However, in this situation you should ideally be using the history feature described later in Section~\ref{sec:entrez-webenv}.

\begin{verbatim}
>>> idlist = ",".join(record["IdList"][:5])
>>> print(idlist)
187237168,187372713,187372690,187372688,187372686
>>> handle = Entrez.efetch(db="nucleotide", id=idlist, retmode="xml")
>>> records = Entrez.read(handle)
>>> len(records)
5
\end{verbatim}
Each of these records corresponds to one GenBank record.
\begin{verbatim}
>>> print(records[0].keys())
[u'GBSeq_moltype', u'GBSeq_source', u'GBSeq_sequence',
 u'GBSeq_primary-accession', u'GBSeq_definition', u'GBSeq_accession-version',
 u'GBSeq_topology', u'GBSeq_length', u'GBSeq_feature-table',
 u'GBSeq_create-date', u'GBSeq_other-seqids', u'GBSeq_division',
 u'GBSeq_taxonomy', u'GBSeq_references', u'GBSeq_update-date',
 u'GBSeq_organism', u'GBSeq_locus', u'GBSeq_strandedness']

>>> print(records[0]["GBSeq_primary-accession"])
DQ110336

>>> print(records[0]["GBSeq_other-seqids"])
['gb|DQ110336.1|', 'gi|187237168']

>>> print(records[0]["GBSeq_definition"])
Cypripedium calceolus voucher Davis 03-03 A maturase (matR) gene, partial cds;
mitochondrial

>>> print(records[0]["GBSeq_organism"])
Cypripedium calceolus
\end{verbatim}

You could use this to quickly set up searches -- but for heavy usage, see Section~\ref{sec:entrez-webenv}.

\subsection{Searching, downloading, and parsing GenBank records}
\label{sec:entrez-search-fetch-genbank}

The GenBank record format is a very popular method of holding information about sequences, sequence features, and other associated sequence information. The format is a good way to get information from the NCBI databases at \url{http://www.ncbi.nlm.nih.gov/}.

In this example we'll show how to query the NCBI databases,to retrieve the records from the query, and then parse them using \verb+Bio.SeqIO+  - something touched on in Section~\ref{sec:SeqIO_GenBank_Online}.
For simplicity, this example \emph{does not} take advantage of the WebEnv history feature -- see Section~\ref{sec:entrez-webenv} for this.

First, we want to make a query and find out the ids of the records to retrieve. Here we'll do a quick search for one of our favorite organisms, \emph{Opuntia} (prickly-pear cacti). We can do quick search and get back the GIs (GenBank identifiers) for all of the corresponding records. First we check how many records there are:

\begin{verbatim}
>>> from Bio import Entrez
>>> Entrez.email = "A.N.Other@example.com"     # Always tell NCBI who you are
>>> handle = Entrez.egquery(term="Opuntia AND rpl16")
>>> record = Entrez.read(handle)
>>> for row in record["eGQueryResult"]:
...     if row["DbName"]=="nuccore":
...         print(row["Count"])
...
9
\end{verbatim}
Now we download the list of GenBank identifiers:
\begin{verbatim}
>>> handle = Entrez.esearch(db="nuccore", term="Opuntia AND rpl16")
>>> record = Entrez.read(handle)
>>> gi_list = record["IdList"]
>>> gi_list
['57240072', '57240071', '6273287', '6273291', '6273290', '6273289', '6273286',
'6273285', '6273284']
\end{verbatim}

Now we use these GIs to download the GenBank records - note that with older versions of Biopython you had to supply a comma separated list of GI numbers to Entrez, as of Biopython 1.59 you can pass a list and this is converted for you:

\begin{verbatim}
>>> gi_str = ",".join(gi_list)
>>> handle = Entrez.efetch(db="nuccore", id=gi_str, rettype="gb", retmode="text")
\end{verbatim}

If you want to look at the raw GenBank files, you can read from this handle and print out the result:

\begin{verbatim}
>>> text = handle.read()
>>> print(text)
LOCUS       AY851612                 892 bp    DNA     linear   PLN 10-APR-2007
DEFINITION  Opuntia subulata rpl16 gene, intron; chloroplast.
ACCESSION   AY851612
VERSION     AY851612.1  GI:57240072
KEYWORDS    .
SOURCE      chloroplast Austrocylindropuntia subulata
  ORGANISM  Austrocylindropuntia subulata
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            Caryophyllales; Cactaceae; Opuntioideae; Austrocylindropuntia.
REFERENCE   1  (bases 1 to 892)
  AUTHORS   Butterworth,C.A. and Wallace,R.S.
...
\end{verbatim}

In this case, we are just getting the raw records. To get the records in a more Python-friendly form, we can use \verb+Bio.SeqIO+ to parse the GenBank data into \verb|SeqRecord| objects, including \verb|SeqFeature| objects (see Chapter~\ref{chapter:Bio.SeqIO}):

\begin{verbatim}
>>> from Bio import SeqIO
>>> handle = Entrez.efetch(db="nuccore", id=gi_str, rettype="gb", retmode="text")
>>> records = SeqIO.parse(handle, "gb")
\end{verbatim}

\noindent We can now step through the records and look at the information we are interested in:
\begin{verbatim}
>>> for record in records:
>>> ...    print("%s, length %i, with %i features" \
>>> ...           % (record.name, len(record), len(record.features)))
AY851612, length 892, with 3 features
AY851611, length 881, with 3 features
AF191661, length 895, with 3 features
AF191665, length 902, with 3 features
AF191664, length 899, with 3 features
AF191663, length 899, with 3 features
AF191660, length 893, with 3 features
AF191659, length 894, with 3 features
AF191658, length 896, with 3 features
\end{verbatim}

Using these automated query retrieval functionality is a big plus over doing things by hand.   Although the module should obey the NCBI's max three queries per second rule, the NCBI have other recommendations like avoiding peak hours.  See Section~\ref{sec:entrez-guidelines}.
In particular, please note that for simplicity, this example does not use the WebEnv history feature.  You should use this for any non-trivial search and download work, see Section~\ref{sec:entrez-webenv}.

Finally, if plan to repeat your analysis, rather than downloading the files from the NCBI and parsing them immediately (as shown in this example), you should just download the records \emph{once} and save them to your hard disk, and then parse the local file.

\subsection{Finding the lineage of an organism}

Staying with a plant example, let's now find the lineage of the Cypripedioideae orchid family. First, we search the Taxonomy database for Cypripedioideae, which yields exactly one NCBI taxonomy identifier:
\begin{verbatim}
>>> from Bio import Entrez
>>> Entrez.email = "A.N.Other@example.com"     # Always tell NCBI who you are
>>> handle = Entrez.esearch(db="Taxonomy", term="Cypripedioideae")
>>> record = Entrez.read(handle)
>>> record["IdList"]
['158330']
>>> record["IdList"][0]
'158330'
\end{verbatim}
Now, we use \verb+efetch+ to download this entry in the Taxonomy database, and then parse it:
\begin{verbatim}
>>> handle = Entrez.efetch(db="Taxonomy", id="158330", retmode="xml")
>>> records = Entrez.read(handle)
\end{verbatim}
Again, this record stores lots of information:
\begin{verbatim}
>>> records[0].keys()
[u'Lineage', u'Division', u'ParentTaxId', u'PubDate', u'LineageEx',
 u'CreateDate', u'TaxId', u'Rank', u'GeneticCode', u'ScientificName',
 u'MitoGeneticCode', u'UpdateDate']
\end{verbatim}
We can get the lineage directly from this record:
\begin{verbatim}
>>> records[0]["Lineage"]
'cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina;
 Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta;
 Liliopsida; Asparagales; Orchidaceae'
\end{verbatim}

The record data contains much more than just the information shown here - for example look under \texttt{"LineageEx"} instead of \texttt{"Lineage"} and you'll get the NCBI taxon identifiers of the lineage entries too.

\section{Using the history and WebEnv}
\label{sec:entrez-webenv}

Often you will want to make a series of linked queries.  Most typically,
running a search, perhaps refining the search, and then retrieving detailed
search results.  You \emph{can} do this by making a series of separate calls
to Entrez.  However, the NCBI prefer you to take advantage of their history
support - for example combining ESearch and EFetch.

Another typical use of the history support would be to combine EPost and
EFetch.  You use EPost to upload a list of identifiers, which starts a new
history session.  You then download the records with EFetch by referring
to the session (instead of the identifiers).

\subsection{Searching for and downloading sequences using the history}
Suppose we want to search and download all the \textit{Opuntia} rpl16
nucleotide sequences, and store them in a FASTA file.  As shown in
Section~\ref{sec:entrez-search-fetch-genbank}, we can naively combine
\verb|Bio.Entrez.esearch()| to get a list of GI numbers, and then call
\verb|Bio.Entrez.efetch()| to download them all.

However, the approved approach is to run the search with the history
feature.  Then, we can fetch the results by reference to the search
results - which the NCBI can anticipate and cache.

To do this, call \verb|Bio.Entrez.esearch()| as normal, but with the
additional argument of \verb|usehistory="y"|,

\begin{verbatim}
>>> from Bio import Entrez
>>> Entrez.email = "history.user@example.com"
>>> search_handle = Entrez.esearch(db="nucleotide",term="Opuntia[orgn] and rpl16",
                                   usehistory="y")
>>> search_results = Entrez.read(search_handle)
>>> search_handle.close()
\end{verbatim}

\noindent When you get the XML output back, it will still include the usual search results:

\begin{verbatim}
>>> gi_list = search_results["IdList"]
>>> count = int(search_results["Count"])
>>> assert count == len(gi_list)
\end{verbatim}

\noindent However, you also get given two additional pieces of information, the {\tt WebEnv} session cookie, and the {\tt QueryKey}:

\begin{verbatim}
>>> webenv = search_results["WebEnv"]
>>> query_key = search_results["QueryKey"]
\end{verbatim}

Having stored these values in variables {\tt session\_cookie} and {\tt query\_key} we can use them as parameters to \verb|Bio.Entrez.efetch()| instead of giving the GI numbers as identifiers.

While for small searches you might be OK downloading everything at once, it is better to download in batches.  You use the {\tt retstart} and {\tt retmax} parameters to specify which range of search results you want returned (starting entry using zero-based counting, and maximum number of results to return).  Sometimes you will get intermittent errors from Entrez, HTTPError 5XX, we use a try except pause retry block to address this.
For example,

\begin{verbatim}
from Bio import Entrez
import time
try:
    from urllib.error import HTTPError  # for Python 3
except ImportError:
    from urllib2 import HTTPError  # for Python 2
batch_size = 3
out_handle = open("orchid_rpl16.fasta", "w")
for start in range(0, count, batch_size):
    end = min(count, start+batch_size)
    print("Going to download record %i to %i" % (start+1, end))
    attempt = 1
    while attempt <= 3:
        try:
            fetch_handle = Entrez.efetch(db="nucleotide", rettype="fasta", retmode="text",
                                         retstart=start, retmax=batch_size,
                                         webenv=webenv, query_key=query_key)
        except HTTPError as err:
            if 500 <= err.code <= 599:
                print("Received error from server %s" % err)
                print("Attempt %i of 3" % attempt)
                attempt += 1
                time.sleep(15)
            else:
                raise
    data = fetch_handle.read()
    fetch_handle.close()
    out_handle.write(data)
out_handle.close()
\end{verbatim}

\noindent For illustrative purposes, this example downloaded the FASTA records in batches of three.  Unless you are downloading genomes or chromosomes, you would normally pick a larger batch size.

\subsection{Searching for and downloading abstracts using the history}
Here is another history example, searching for papers published in the last year about the \textit{Opuntia}, and then downloading them into a file in MedLine format:

\begin{verbatim}
from Bio import Entrez
import time
try:
    from urllib.error import HTTPError  # for Python 3
except ImportError:
    from urllib2 import HTTPError  # for Python 2
Entrez.email = "history.user@example.com"
search_results = Entrez.read(Entrez.esearch(db="pubmed",
                                            term="Opuntia[ORGN]",
                                            reldate=365, datetype="pdat",
                                            usehistory="y"))
count = int(search_results["Count"])
print("Found %i results" % count)

batch_size = 10
out_handle = open("recent_orchid_papers.txt", "w")
for start in range(0,count,batch_size):
    end = min(count, start+batch_size)
    print("Going to download record %i to %i" % (start+1, end))
    attempt = 1
    while attempt <= 3:
        try:
            fetch_handle = Entrez.efetch(db="pubmed",rettype="medline",
                                         retmode="text",retstart=start,
                                         retmax=batch_size,
                                         webenv=search_results["WebEnv"],
                                         query_key=search_results["QueryKey"])
        except HTTPError as err:
            if 500 <= err.code <= 599:
                print("Received error from server %s" % err)
                print("Attempt %i of 3" % attempt)
                attempt += 1
                time.sleep(15)
            else:
                raise
    data = fetch_handle.read()
    fetch_handle.close()
    out_handle.write(data)
out_handle.close()
\end{verbatim}

\noindent At the time of writing, this gave 28 matches - but because this is a date dependent search, this will of course vary.  As described in Section~\ref{subsec:entrez-and-medline} above, you can then use \verb|Bio.Medline| to parse the saved records.

\subsection{Searching for citations}
\label{sec:elink-citations}

Back in Section~\ref{sec:elink} we mentioned ELink can be used to search for citations of a given paper.
Unfortunately this only covers journals indexed for PubMed Central
(doing it for all the journals in PubMed would mean a lot more work for the NIH).
Let's try this for the Biopython PDB parser paper, PubMed ID 14630660:

\begin{verbatim}
>>> from Bio import Entrez
>>> Entrez.email = "A.N.Other@example.com"
>>> pmid = "14630660"
>>> results = Entrez.read(Entrez.elink(dbfrom="pubmed", db="pmc",
...                                    LinkName="pubmed_pmc_refs", id=pmid))
>>> pmc_ids = [link["Id"] for link in results[0]["LinkSetDb"][0]["Link"]]
>>> pmc_ids
['2744707', '2705363', '2682512', ..., '1190160']
\end{verbatim}

Great - eleven articles. But why hasn't the Biopython application note been
found (PubMed ID 19304878)? Well, as you might have guessed from the variable
names, there are not actually PubMed IDs, but PubMed Central IDs. Our
application note is the third citing paper in that list, PMCID 2682512.

So, what if (like me) you'd rather get back a list of PubMed IDs? Well we
can call ELink again to translate them. This becomes a two step process,
so by now you should expect to use the history feature to accomplish it
(Section~\ref{sec:entrez-webenv}).

But first, taking the more straightforward approach of making a second
(separate) call to ELink:

\begin{verbatim}
>>> results2 = Entrez.read(Entrez.elink(dbfrom="pmc", db="pubmed", LinkName="pmc_pubmed",
...                                     id=",".join(pmc_ids)))
>>> pubmed_ids = [link["Id"] for link in results2[0]["LinkSetDb"][0]["Link"]]
>>> pubmed_ids
['19698094', '19450287', '19304878', ..., '15985178']
\end{verbatim}

\noindent This time you can immediately spot the Biopython application note
as the third hit (PubMed ID 19304878).

Now, let's do that all again but with the history \ldots
\textit{TODO}.

And finally, don't forget to include your \emph{own} email address in the Entrez calls.
